BN1939 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 3.3132e-05 1.0005e-02
Layer 3 5.0616e-04 4.0243e-02
WM 6.4954e-04 3.3264e-02
Layer 6 8.4944e-04 6.5943e-03
Layer 5 1.1710e-03 7.5278e-03
Layer 2 1.2891e-03 1.1131e-01
Layer 1 4.8435e-01 4.9719e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.0918 0.5919
SH3GL2 Layer 6 2.1484 0.4377
CPLX1 Layer 5 2.1875 0.4317
SLC24A2 Layer 4 2.1289 0.4217
PFKP Layer 5 2.3184 0.4073
SYNGR1 Layer 4 2.0625 0.4018
ELAVL2 Layer 4 1.9805 0.3949
PLEKHB2 Layer 4 2.0781 0.3947
NUDT4 Layer 5 2.0039 0.3943
UBE2D3 Layer 4 1.9629 0.3929
COX7A1 Layer 6 2.1973 0.3927
EFHD2 Layer 6 2.2617 0.3922
B4GAT1 Layer 5 1.9990 0.3876
ATP5MF Layer 4 1.9404 0.3838
LGALS1 Layer 5 2.1191 0.3831
SNAP91 Layer 4 2.0547 0.3818
ARHGDIG Layer 5 2.1816 0.3818
ITPK1 WM 2.1973 0.3811
CTSD Layer 5 2.0176 0.3803
SEZ6L2 Layer 5 1.9629 0.3798
STX1A Layer 4 2.2832 0.3796
MAP1LC3A Layer 5 1.9580 0.3792
MAPK8IP3 Layer 5 1.8545 0.3785
UBA1 Layer 5 2.0176 0.3755
SLC25A22 Layer 5 2.1680 0.3743
ATP6V1A Layer 5 1.9189 0.3724
TAGLN3 Layer 4 1.9580 0.3722
DPY19L1 Layer 5 1.9805 0.3713
DCLK1 Layer 6 2.0254 0.3699
EPHB6 Layer 5 2.1016 0.3685
PAIP2 WM 1.8750 0.3681
BEX4 Layer 6 2.0015 0.3672
OAT Layer 4 2.0117 0.3670
MYL6B Layer 5 2.0039 0.3666
APBB1 WM 1.8887 0.3662
PFN2 Layer 5 2.0117 0.3641
EPS15 Layer 4 1.8418 0.3630
CNTNAP1 Layer 5 2.0488 0.3628
BCL11A Layer 5 1.9990 0.3626
PHF24 Layer 5 2.0254 0.3619
GABRA5 Layer 6 2.1250 0.3619
SLC35F1 Layer 6 2.0449 0.3609
CLTA Layer 5 1.8242 0.3604
BMERB1 Layer 4 2.1621 0.3599
SLIT1 Layer 6 1.9766 0.3598
STMN2 Layer 5 2.1289 0.3596
HS3ST2 Layer 6 2.1797 0.3594
OTUB1 Layer 5 1.8672 0.3593
UQCRC1 Layer 5 1.9766 0.3584
PSMB7 Layer 6 1.7832 0.3571

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1939
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1939_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1939/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1939/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1939/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1939/report/PD/BN1939_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1939/report/PD/BN1939_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 09:55:44
  • Number of Processes: 10
  • Spending Time: 0h 5m